GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Paraburkholderia bryophila 376MFSha3.1

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate H281DRAFT_04551 H281DRAFT_04551 acetolactate synthase, large subunit

Query= metacyc::MONOMER-18810
         (585 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04551 H281DRAFT_04551
           acetolactate synthase, large subunit
          Length = 587

 Score =  951 bits (2458), Expect = 0.0
 Identities = 455/585 (77%), Positives = 522/585 (89%)

Query: 1   MPSAEFSHADSNSSAAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEH 60
           MPSAEFS +D+      + IGA +L+ ALA+E VE+VWGYPGG+VLYIYDEL+KQ KF+H
Sbjct: 3   MPSAEFSTSDTTPQHEADSIGATVLMKALADEDVEFVWGYPGGSVLYIYDELYKQDKFQH 62

Query: 61  ILVRHEQAAVHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPT 120
           ILVRHEQAAVHAAD Y+R+TGKVGV LVTSGPGVTNAVTGIATAY+DSIPMVVI+G VPT
Sbjct: 63  ILVRHEQAAVHAADAYSRSTGKVGVCLVTSGPGVTNAVTGIATAYMDSIPMVVISGQVPT 122

Query: 121 HAIGQDAFQECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDV 180
            AIGQDAFQECDTVGITRP VKHNFLVKDVRDLAAT+KKAF+IA TGRPGPV++DIPKDV
Sbjct: 123 AAIGQDAFQECDTVGITRPCVKHNFLVKDVRDLAATVKKAFYIARTGRPGPVLIDIPKDV 182

Query: 181 SRNACKYEYPKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELR 240
           S+  C+YE  K++ +RSYNPV KGHSGQIRKAV+LL  A+RPYIYTGGG++LA+AS EL 
Sbjct: 183 SKAPCQYEPIKTVSLRSYNPVTKGHSGQIRKAVSLLLSAKRPYIYTGGGIILADASRELN 242

Query: 241 QLAALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRV 300
           Q A L G+P+TNTLMGLG +  + K+F+GMLGMHGTYEANMAMQ+CDVLIAIGARFDDRV
Sbjct: 243 QFADLLGYPITNTLMGLGGYRASDKKFLGMLGMHGTYEANMAMQHCDVLIAIGARFDDRV 302

Query: 301 IGNPAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREA 360
           IG+PAHF S+ RKIIHIDIDPSSISKRVKVDIPIVG+VK+VL+ELI Q++ ++  P   A
Sbjct: 303 IGDPAHFASRPRKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQTAEHGPDTAA 362

Query: 361 LAKWWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFY 420
           LA WW+ IE WR+ DCLK+DR S++IKPQYVVEK WELT G+AF+CSDVGQHQMWAAQFY
Sbjct: 363 LADWWKDIEAWRAKDCLKFDRKSDVIKPQYVVEKAWELTDGNAFVCSDVGQHQMWAAQFY 422

Query: 421 KFDEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDT 480
           +F++PRRWINSGGLGTMG GLP AMG+K A P+ +V+ ITGEGSIQMCIQELSTC QY+T
Sbjct: 423 RFNKPRRWINSGGLGTMGFGLPAAMGVKMAHPDDDVLCITGEGSIQMCIQELSTCKQYET 482

Query: 481 PVKICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEP 540
           PVKI SLNN YLGMVRQWQ+IEY  RYSHSYMDALPDFVKLAEAYGHVGMR+E+T+DVEP
Sbjct: 483 PVKIISLNNRYLGMVRQWQQIEYSKRYSHSYMDALPDFVKLAEAYGHVGMRIERTADVEP 542

Query: 541 ALREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           AL+EA RLKDRTVFLDFQTDPTENVWPMVQAGKGI+EML+G+EDL
Sbjct: 543 ALKEALRLKDRTVFLDFQTDPTENVWPMVQAGKGITEMLMGSEDL 587


Lambda     K      H
   0.319    0.135    0.407 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1064
Number of extensions: 25
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 585
Length of database: 587
Length adjustment: 37
Effective length of query: 548
Effective length of database: 550
Effective search space:   301400
Effective search space used:   301400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate H281DRAFT_04551 H281DRAFT_04551 (acetolactate synthase, large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00118.hmm
# target sequence database:        /tmp/gapView.29001.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                    Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.8e-261  854.3   0.0   2.2e-261  854.1   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04551  H281DRAFT_04551 acetolactate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04551  H281DRAFT_04551 acetolactate synthase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  854.1   0.0  2.2e-261  2.2e-261       3     554 ..      23     581 ..      21     584 .. 0.98

  Alignments for each domain:
  == domain 1  score: 854.1 bits;  conditional E-value: 2.2e-261
                                    TIGR00118   3 gaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvv 67 
                                                  ga++l+++l +e+ve v+GyPGG+vl iyd+ly +++++hilvrheqaa+haad y+r++GkvGv+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04551  23 GATVLMKALADEDVEFVWGYPGGSVLYIYDELYkQDKFQHILVRHEQAAVHAADAYSRSTGKVGVC 88 
                                                  899******************************999****************************** PP

                                    TIGR00118  68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaed 133
                                                  l+tsGPG tn+vtgiatay+ds+P+vv++Gqv+t++iG+dafqe+d +Git+p++kh+flvk+++d
  lcl|FitnessBrowser__Burk376:H281DRAFT_04551  89 LVTSGPGVTNAVTGIATAYMDSIPMVVISGQVPTAAIGQDAFQECDTVGITRPCVKHNFLVKDVRD 154
                                                  ****************************************************************** PP

                                    TIGR00118 134 lpeilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliek 199
                                                  l++++k+af+ia tGrPGPvl+d+Pkdv++a +++e  ++v+l++y+p +kgh  qi+ka+ l+ +
  lcl|FitnessBrowser__Burk376:H281DRAFT_04551 155 LAATVKKAFYIARTGRPGPVLIDIPKDVSKAPCQYEPIKTVSLRSYNPVTKGHSGQIRKAVSLLLS 220
                                                  ****************************************************************** PP

                                    TIGR00118 200 akkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavs 265
                                                  ak+P ++ GgG+i a+as+el+++a+ l  p+t tl+GlG++ + ++++lgmlGmhGt+ean+a++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04551 221 AKRPYIYTGGGIILADASRELNQFADLLGYPITNTLMGLGGYRASDKKFLGMLGMHGTYEANMAMQ 286
                                                  ****************************************************************** PP

                                    TIGR00118 266 eadlliavGarfddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklk 330
                                                  ++d+lia+Garfddrv g+ a+fa++  kiihididP++i+k vkvdipivGd+k+vl+el+++l+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04551 287 HCDVLIAIGARFDDRVIGDPAHFASRPrKIIHIDIDPSSISKRVKVDIPIVGDVKEVLKELIEQLQ 352
                                                  ************************98626***********************************99 PP

                                    TIGR00118 331 ee....ekkeke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwa 391
                                                  +     ++     W++ ie w+++ +lk+d++++ ikPq+v+++ ++l++++a+v +dvGqhqmwa
  lcl|FitnessBrowser__Burk376:H281DRAFT_04551 353 TAehgpDTAALAdWWKDIEAWRAKDCLKFDRKSDVIKPQYVVEKAWELTDGNAFVCSDVGQHQMWA 418
                                                  9866653333335***************************************************** PP

                                    TIGR00118 392 aqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipv 457
                                                  aqfy+++kpr++i+sgGlGtmGfGlPaa+G+k+a+p+++v+++tG+gs+qm +qelst+++y++pv
  lcl|FitnessBrowser__Burk376:H281DRAFT_04551 419 AQFYRFNKPRRWINSGGLGTMGFGLPAAMGVKMAHPDDDVLCITGEGSIQMCIQELSTCKQYETPV 484
                                                  ****************************************************************** PP

                                    TIGR00118 458 kivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkeale 523
                                                  ki+ lnn++lGmv+qWq++ y++rys++++ + lpdfvklaeayG++g+rie+ +++e +lkeal+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04551 485 KIISLNNRYLGMVRQWQQIEYSKRYSHSYMDA-LPDFVKLAEAYGHVGMRIERTADVEPALKEALR 549
                                                  *******************************5.********************************9 PP

                                    TIGR00118 524 sk.epvlldvevdkeeevlPmvapGagldelv 554
                                                   k + v+ld++ d +e+v+Pmv  G+g++e++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04551 550 LKdRTVFLDFQTDPTENVWPMVQAGKGITEML 581
                                                  88689*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (587 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.76
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory